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quick:pbspro [2014/05/14 10:37]
ischeepers 		quick:pbspro [2025/09/22 17:47] (current)
kevin [Example 4 : empty job]
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 ====== Job submission using PBSPro ====== ====== Job submission using PBSPro ======
  
-As of January 2014, CHPC has a new scheduler - PBSPro.+The CHPC system uses the PBSPro scheduler.
  
-Main user documentation can be found at http://resources.altair.com/pbs/documentation/support/PBSProUserGuide12.1.pdf+Main user documentation can be found at [[https://www.altair.com/pbs-works-documentation/|Altair]]
  
 But here is a summary of how to submit jobs at CHPC. But here is a summary of how to submit jobs at CHPC.
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   *     ''qstat'' see all jobs and their status   *     ''qstat'' see all jobs and their status
   *     ''qdel'' delete a job   *     ''qdel'' delete a job
-  *     ''qalter'' modify options on a pending job +  *     ''qalter'' modify options on a pending job           
 +  * ''qsig'' send a signal to a job (eg. to terminate it)  
  
  
 ====How to submit a batch job==== ====How to submit a batch job====
  
-Use the qsub command to submit a script file. PBSPro job file allows for specification of options at the beginning of the file prefaced by the #PBS delimiter followed by PBS commands. Commands will be executed in the order given in the script.+Use the ''qsub'' command to submit a script file to the scheduler. PBS-Pro jobs can be controlled using command line switches, //or// directives in the job submission file prefaced by the ''#PBS'' keyword. 
  
-A script can include just about anything which you could do during a terminal session such as set environment variables, change directories, and move files. See the qsub man page for a complete list of options.+See the ''qsub'' man page for a complete list of options. 
  
-''qsub myscriptname''+The first line of a script file may specify the interpreter, eg., bash is selected by using ''#!/bin/bash'' as the first line of the job script file.
  
-=== Example PBS scripts === +A script can include just about anything which you could do during a terminal session such as set environment variables, change directories, and move files. 
-Job submission scripts are shell scripts with PBS directives in comments. +
  
-**PLEASE NOTE!** The first line should always have the hash-bang and shell path, eg. **#!/bin/bash** or **#!/bin/sh**+> Job script files can be named to anything allowed for a regular file, but it is strongly recommended that you use ''.pbs'' as the file extension to make it easy to distinguish job scripts from other shell scripts (''.sh'').
  
-On a cluster system, run an executable on 3 nodes using all 8 cores per node with 8 MPI processes for 5 hours: 
  
-<code> +====How to start an interactive job on a compute node====
-#!/bin/bash +
-#PBS -j oe +
-#PBS -l walltime=5:00:00 +
-#PBS -l select=3:ncpus=8:mpiprocs=8 +
-#PBS -V +
-cd $HOME/scratch5 +
-</code>+
  
-On a non-cluster system, run an executable on 24 cores for 5 hours+''qsub -I -V''
  
-<code> +to start an interactive session, retaining all environment variables.
-#!/bin/bash +
-#PBS -j oe +
-#PBS -l walltime=5:00:00 +
-#PBS -l ncpus=24 +
-#PBS -V +
-cd $HOME/scratch5 +
-</code>+
  
-===How long can a job run=== 
  
-There is no limit to the amount of time that a PBS job can run. If no time limit is specified, a default of 12 hours is assigned. Remember to check point long running jobs.+====How to monitor job submissions to the queue====
  
-To specify a time, include the following line in the submission script:+The job number will be returned if the job has been accepted by the scheduler. Use this 
 +number to check on the progress of a specific job:
  
-''#PBS -l walltime=hhhh:mm:ss''+''qstat -f <jobnum>''
  
-===Exclusive use of cluster nodes===+To inspect jobs that have already finished:
  
-On cluster systems, if a job does not request all the cores on a node, it is possible another job will share the same node. To prevent this, request exclusive use.+''qstat -x -f <jobnum>''
  
-''#PBS -l place=excl''+or
  
-===How to export interactive session environment to job===+''qstat -xf <jobnum>''
  
-To include the shell environment in the batch job, either use the -V option with qsub or as a PBS directive+====How to monitor job arrays====
  
-''qsub -V'' +To see the array job status on the queue, postfix the 
-         +jobnumber with empty square brackets:
-''#PBS -V''+
  
-===Hyper-Threading===+''qstat -J <jobnum>[]''
  
-On the CHPC cluster, Hyperthreading is disabled, except on the MIC nodes. 
  
-===Suppose I want to do a parameter study. How do I submit all these jobs with a different value of parameter?===+To look at one specific job in the array, add ''-t'' to the qstat arguments:
  
-Use PBS Job Arrays. You can specify how many jobs to run by adding the directive+''qstat -xft <jobnum>[array-index]''
  
-#PBS -J <range> 
  
-where range is X-Y:Z. So 1-10:2 indicates all the even jobs from 1 to 10, i.e., 2,4,6,8 and 10.+eg
  
-PBS defines two environment variables:+''qstat -xft 967890[2]''
  
-PBS_ARRAY_INDEX     job array index 
-PBS_ARRAY_ID        job array id 
  
-These variables are also defined as attributes: 
  
-array_index +=====PBS-Pro Job Exit Codes =====
-array_id+
  
-Based on the job array index, different input files can be used for each job in the job array. Below is a job script example that submits two jobs, each using one processor.+====Job Exit Codes Between 0 and 128 (or 256)==== 
 +This is the exit value of the top process in the job, typically the shell. This may be the exit value of the last command executed in the shell or the .logout script if the user has such a script (csh).
  
-NOTE: The PBS directives specify the resources that will be used by EACH individual job, NOT all the jobs together.+====Job Exit Codes >= 128 (or 256)==== 
 +This means the job was killed by the PBS scheduler by sending it a signal. 
  
-<code> +The **modulo** or **remainder** operator [[http://en.wikipedia.org/wiki/Modulo_operation]] is used to interpret (or “decode”) PBS job exit values. 
-#!/bin/sh +
-#PBS -V +
-#PBS -l select=1:ncpus=1:mpiprocs=1,walltime=48:00 +
-#PBS -N Job_Array_Test +
-#PBS -j oe -o ja.^array_index^.pbs +
-#PBS -J 1-2 +
-cd $PBS_O_WORKDIR +
-# +
-unset echo +
-              +
-echo $PBS_ARRAY_INDEX +
-                +
-echo $PBS_ARRAY_ID $PBS_ARRAY_INDEX >> ja.$PBS_ARRAY_INDEX.out +
-echo ' '        >> ja.$PBS_ARRAY_INDEX.out +
-bin/pi < pi.inp >> ja.$PBS_ARRAY_INDEX.out +
-                 +
-exit +
-</code>+
  
-===How do I determine the number of cores I have requested in my job script?=== 
  
-To determine the number of cores requested, include the following line in the submission script:+The signal is given by X modulo 128 (or 256). An exit value of 137 means the job's top process was killed with signal 9 because ''137 mod 128 = 9''. 
  
-''set NCORES = `cat $PBS_NODEFILE | wc -l`''+Depending on the system, a value greater than 128 or 256, see ''man wait(2)'', is the signal that was sent by PBS-Pro to kill the job. (i.e., 265 mod 256 = 9 or 271 mod 256 = 15.) 
  
-===How do I determine the number of nodes I have requested in my job script?===+Exit code 271 means that the job exceeded the limit requested at submission, eg. walltime or cpu usage, and was killed.
  
-To determine the number of nodes requested, include the following line in the submission script:+See ''man kill'' for a mapping of signal numbers to signal name on your operating system. 
 +====Terminate a job by signal==== 
 +Send a signal to the job
  
-''set NNODES  = `cat $PBS_NODEFILE | uniq | wc -l `''+'' qsig -s SIGTERM  <jobnum>  ''
  
-===A job submitted to the queue is not running=== 
  
-Look at the job status with qstat. The next to last line of the output is a comment describing the job status. Possible outputs include:+===== Examples: PBS-Pro job submission scripts =====
  
-''qstat -f yourjobid''+[[howto:PBS-Pro_job_submission_examples]]
  
-  *  Job run at date at time on hostname +===== Examples: Gaussian jobs =====
-        Job is running OK +
  
-  *  Not Running: No available resources on nodes 
-        Job requires more memory,cores, or processors than currently available, or you have requested more resources than what physically exists on the system.  
  
-  *  Job held, too many failed attempts to run +[[howto:gaussian|Gaussian Single and Multi-Node Scripts]] 
-        Delete and resubmit job+    
 +   
  
-If this persists, contact User support  
  
-  *  Not Running, Draining system to allow starving job to run 
-        Job will not run because the resources are reserved for other jobs.  
  
-===Queued Jobs stuck in an error state (E)=== 
  
-Try deleting the job with qdel 
  
-''qdel -Wforce yourjobid''+===== Examples: Amber jobs =====
  
-The following must be **plain text** files, as created by unix programs like ''nano'' or ''vi''. If you wish to create them on your desktop and copy them over, ensure they contain no formatting and have unix line endings. Microsoft Word would be a bad choice. 
  
-===== Example 1 : Gaussian job on 1 node ===== +[[howto:amber|Amber job submission scripts]]
-<file bash gaussian_single.qsub>+
  
-#! /bin/sh 
-#PBS -N eric.job 
-#PBS -l select=1:ncpus=12:jobtype=dell,place=free:group=nodetype 
-#PBS -l walltime=1:00:00 
-#PBS -q workq 
-#PBS -m abe 
-#PBS -o /export/home/username/scratch/gaussian.out 
-#PBS -e /export/home/username/scratch/gaussian.err 
-#PBS -M username@email 
  
-cd $PBS_O_WORKDIR 
-source /etc/profile.d/modules.sh 
-module add gaussian/g09.D01 
-g09 < eric.inp > eric.log 
-</file> 
  
-===== Example 2 : Gaussian job on more than 1 node ===== +===== Example: Quantum Espresso =====
-<file bash gaussian_multiple.qsub>+
  
-#!/bin/bash 
-#PBS -N eric.job 
-#PBS -l select=2:ncpus=12:jobtype=dell,place=free:group=nodetype 
-#PBS -l walltime=12:00:00 
-#PBS -q workq  
-#PBS -m abe 
-#PBS -o /export/home/embele/scratch/eric/cow/viw.out 
-#PBS -e /export/home/embele/scratch/eric/cow/viw.err 
-#PBS -M username@email 
  
-cd $PBS_O_WORKDIR+[[howto:quantum_espresso|Quantum Espresso]]
  
-echo "My job start here" 
-date 
-pwd 
  
-source /etc/profile.d/modules.sh +===== Example 4 : empty job =====
-module add gaussian/g09.D01 +
-source /opt/gridware/applications/gaussian/g09/bsd/g09.profile +
- +
-LINDA=`cat $PBS_NODEFILE | uniq | tr '\n' "," | sed 's|,$||' ` +
-echo linda: $LINDA +
-cat viw.inp | sed "s/LINDA/$LINDA/" > temp$$.inp +
-g09 < temp$$.inp > OUTPUT_FILE.log +
- +
- +
-echo "My job ends here" +
-date +
- +
-where viw.inp is my input file +
- +
-Your input file should look like this :- +
- +
-%chk=viw.chk +
-%nprocshared=12 +
-%mem=32GB +
-%lindaworkers=LINDA +
- +
- +
- +
-</file> +
-===== Example 2 (a) :  Amber job on GPU nodes ===== +
- +
-<code> +
-#! /bin/sh +
-#PBS -N eric.job +
-#PBS -l select=1:ncpus=12:mpiprocs=12 +
-#PBS -l walltime=1:00:00 +
-#PBS -q kepla_k20 +
-#PBS -m be +
-#PBS -o /export/home/username/amber/amber12/eric.out +
-#PBS -e /export/home/username/amber/amber12/eric.err +
-#PBS -M email@mail.com +
- +
-cd $PBS_O_WORKDIR +
- +
-pwd +
-echo "My job starts here" +
-date +
-source /etc/profile.d/modules.sh +
-module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20 +
-module add amber/k20 +
- +
-exe=pmemd.cuda.MPI +
-nproc=`cat $PBS_NODEFILE|wc -l` +
-time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i mdin -o mdout -p prmtop -c inpcrd +
-echo "My job ends here" +
-date +
-</code> +
- +
-===== Example 2 (b) :  Amber job on normal nodes (Please use this for python,sander and other executables that do not work on GPU===== +
- +
-<code> +
-#! /bin/sh +
-#PBS -N eric.job +
-#PBS -l select=1:ncpus=12:mpiprocs=12 +
-#PBS -l walltime=1:00:00 +
-#PBS -q workq +
-#PBS -m be +
-#PBS -o /export/home/username/amber/amber12/eric.out +
-#PBS -e /export/home/username/amber/amber12/eric.err +
-#PBS -M email@mail.com +
- +
-cd $PBS_O_WORKDIR +
- +
-pwd +
- +
-source /etc/profile.d/modules.sh +
-module add intel-XE/13.0 openmpi/openmpi-1.6.5-intel amber/12 +
- +
-echo "My job starts here" +
-date +
- +
-exe=sander.MPI +
- +
-nproc=`cat $PBS_NODEFILE|wc -l` +
-time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i mdin -o mdout -p prmtop -c inpcrd +
-echo "My job ends here" +
-date +
-</code> +
- +
-===== Example 3 : Quantum Espresso job ===== +
- +
-<code> +
-#!/bin/sh +
-###These lines are for PBSpro +
-#PBS -N QEspresso +
-#PBS -l select=2:ncpus=12:mpiprocs=12:jobtype=dell,place=free:group=nodetype:excl +
-#PBS -l walltime=24:00:00 +
-#PBS -q workq +
-#PBS -m be +
-#PBS -o /export/home/username/scratch/run-directory/stdout +
-#PBS -e /export/home/username/scratch/run-directory/stderr +
-#PBS -V +
-##### Environment Settings +
-source /etc/profile.d/modules.sh +
-module add intel-XE/13.0 +
-module add QEspresso/5.0.2 +
-##### Running commands +
-NP=`cat $PBS_NODEFILE | wc -l` +
-cd $HOME/scratch5 +
-mpirun -f $PBS_NODEFILE -r ssh -ib -env I_MPI_DEBUG 2 -np $NP pw.x -npool 3  -inp inputfile.inp  +
-</code> +
- +
-===== Example 4 :  empty job =====+
  
 <code> <code>
Line 317: Line 135:
 source /etc/profile.d/modules.sh   # so module command works source /etc/profile.d/modules.sh   # so module command works
 cd $PBS_O_WORKDIR   # change to working directory cd $PBS_O_WORKDIR   # change to working directory
-Where + 
-<jobname> = name of the job +#Where 
-<totalcores>= total number of cores +#<jobname> = name of the job 
-<hosts> = number of hosts +#<totalcores>= total number of cores 
-<architecture> = architecture where the jobs will run (nehalem, westmere, dell) +#<hosts> = number of hosts 
-<queue> = submission queue ( workq , priorityq , specialq , intel_mic , spark , kepla_k20 , accelrys)+#<architecture> = architecture where the jobs will run (nehalem, westmere, dell) 
 +#<queue> = submission queue ( serial, smp, normal, ...,  accelrys) 
 +#<executable> = Binary to be run 
 + 
 +mpirun -np <totalcores> <executable>
  
 </code> </code>
  
-//Note that the M9000 sparc queue is called 'spark'// 
  
-===== MPI example =====+ 
 +===== Example 5 : MPI example =====
  
 Syntax Syntax
Line 338: Line 160:
 ... ...
 </code> </code>
- +===== Further examples ===== 
-For more information on qsub +  * Various [[howto:bioinformatics?&#basic_examples|bioinformatics examples]] illustrate some further possibilities. Specifically the blast examples illustrate job arrays and job dependencies. 
-  $ man qsub +  * This [[howto:gpu_gromacs#pbs_job_script|gromacs example]] shows an interesting case where mpi, openmp and the gpus are used in a single job.
- +
-Additional information on the job queues available  +
-  $ qstat -q +
- +
-A minimal script Dell example would be  +
-  $ more mpirun_basic_example +
-  #PBS -l select=2:ncpus=12:mpiprocs=12:jobtype=dell +
-  cat $PBS_NODEFILE +
- +
- +
-submiting the script +
-  $ qsub mpirun_basic_example +
-The submitted jobs output file should produce output similar to  +
-  cnode-6-33 +
-  ... repeated 11 times ... +
-  cnode-6-34 +
-  ... repeated 11 times ...+
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